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W. James Kent, Ph.D. - Publications

Affiliations: 
2002 University of California, Santa Cruz, Santa Cruz, CA, United States 
Area:
Genetics
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99 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Raney BJ, Barber GP, Benet-Pagès A, Casper J, Clawson H, Cline MS, Diekhans M, Fischer C, Navarro Gonzalez J, Hickey G, Hinrichs AS, Kuhn RM, Lee BT, Lee CM, Le Mercier P, ... ... Kent WJ, et al. The UCSC Genome Browser database: 2024 update. Nucleic Acids Research. PMID 37953330 DOI: 10.1093/nar/gkad987  0.544
2023 Clawson H, Lee BT, Raney BJ, Barber GP, Casper J, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee CM, Nassar LR, Perez G, Wick B, Schmelter D, Speir ML, ... ... Kent WJ, et al. GenArk: towards a million UCSC genome browsers. Genome Biology. 24: 217. PMID 37784172 DOI: 10.1186/s13059-023-03057-x  0.544
2023 Hitz B, Lee JW, Jolanki O, Kagda M, Graham K, Sud P, Gabdank I, Strattan JS, Sloan C, Dreszer T, Rowe L, Podduturi N, Malladi V, Chan E, Davidson J, ... ... Kent WJ, et al. The ENCODE Uniform Analysis Pipelines. Research Square. PMID 37503119 DOI: 10.21203/rs.3.rs-3111932/v1  0.445
2023 Clawson H, Lee BT, Barber GP, Casper J, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee CM, Nassar LR, Perez G, Wick B, Schmelter D, Speir ML, Armstrong J, ... ... Kent WJ, et al. GenArk: Towards a million UCSC Genome Browsers. Research Square. PMID 37066427 DOI: 10.21203/rs.3.rs-2697398/v1  0.58
2022 Nassar LR, Barber GP, Benet-Pagès A, Casper J, Clawson H, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee BT, Lee CM, Muthuraman P, Nguy B, Pereira T, Nejad P, ... ... Kent WJ, et al. The UCSC Genome Browser database: 2023 update. Nucleic Acids Research. PMID 36420891 DOI: 10.1093/nar/gkac1072  0.509
2021 Lee BT, Barber GP, Benet-Pagès A, Casper J, Clawson H, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee CM, Muthuraman P, Nassar LR, Nguy B, Pereira T, Perez G, ... ... Kent WJ, et al. The UCSC Genome Browser database: 2022 update. Nucleic Acids Research. PMID 34718705 DOI: 10.1093/nar/gkab959  0.524
2020 Navarro Gonzalez J, Zweig AS, Speir ML, Schmelter D, Rosenbloom KR, Raney BJ, Powell CC, Nassar LR, Maulding ND, Lee CM, Lee BT, Hinrichs AS, Fyfe AC, Fernandes JD, Diekhans M, ... ... Kent WJ, et al. The UCSC Genome Browser database: 2021 update. Nucleic Acids Research. PMID 33221922 DOI: 10.1093/nar/gkaa1070  0.552
2020 Fernandes JD, Hinrichs AS, Clawson H, Gonzalez JN, Lee BT, Nassar LR, Raney BJ, Rosenbloom KR, Nerli S, Rao AA, Schmelter D, Fyfe A, Maulding N, Zweig AS, Lowe TM, ... ... Kent WJ, et al. The UCSC SARS-CoV-2 Genome Browser. Nature Genetics. PMID 32908258 DOI: 10.1038/S41588-020-0700-8  0.599
2020 Fernandes JD, Zamudio-Hurtado A, Clawson H, Kent WJ, Haussler D, Salama SR, Haeussler M. The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families. Mobile Dna. 11: 13. PMID 32266012 DOI: 10.1186/S13100-020-00208-W  0.564
2019 Lee CM, Barber GP, Casper J, Clawson H, Diekhans M, Gonzalez JN, Hinrichs AS, Lee BT, Nassar LR, Powell CC, Raney BJ, Rosenbloom KR, Schmelter D, Speir ML, Zweig AS, ... ... Kent WJ, et al. UCSC Genome Browser enters 20th year. Nucleic Acids Research. PMID 31691824 DOI: 10.1093/Nar/Gkz1012  0.613
2018 Haeussler M, Zweig AS, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Hinrichs AS, Gonzalez JN, Gibson D, Diekhans M, Clawson H, Casper J, Barber GP, ... ... Kent WJ, et al. The UCSC Genome Browser database: 2019 update. Nucleic Acids Research. PMID 30407534 DOI: 10.1093/Nar/Gky1095  0.584
2017 Casper J, Zweig AS, Villarreal C, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Karolchik D, Hinrichs AS, Haeussler M, Guruvadoo L, Navarro Gonzalez J, Gibson D, ... ... Kent WJ, et al. The UCSC Genome Browser database: 2018 update. Nucleic Acids Research. PMID 29106570 DOI: 10.1093/Nar/Gkx1020  0.619
2016 Tyner C, Barber GP, Casper J, Clawson H, Diekhans M, Eisenhart C, Fischer CM, Gibson D, Gonzalez JN, Guruvadoo L, Haeussler M, Heitner S, Hinrichs AS, Karolchik D, Lee BT, ... ... Kent WJ, et al. The UCSC Genome Browser database: 2017 update. Nucleic Acids Research. PMID 27899642 DOI: 10.1093/Nar/Gkw1134  0.631
2016 Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ. UCSC Data Integrator and Variant Annotation Integrator. Bioinformatics (Oxford, England). PMID 26740527 DOI: 10.1093/Bioinformatics/Btv766  0.453
2015 Speir ML, Zweig AS, Rosenbloom KR, Raney BJ, Paten B, Nejad P, Lee BT, Learned K, Karolchik D, Hinrichs AS, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Fujita PA, ... ... Kent WJ, et al. The UCSC Genome Browser database: 2016 update. Nucleic Acids Research. PMID 26590259 DOI: 10.1093/Nar/Gkv1275  0.611
2015 Miga KH, Eisenhart C, Kent WJ. Utilizing mapping targets of sequences underrepresented in the reference assembly to reduce false positive alignments. Nucleic Acids Research. 43: e133. PMID 26163063 DOI: 10.1093/Nar/Gkv671  0.515
2015 Malladi VS, Erickson DT, Podduturi NR, Rowe LD, Chan ET, Davidson JM, Hitz BC, Ho M, Lee BT, Miyasato S, Roe GR, Simison M, Sloan CA, Strattan JS, Tanaka F, ... Kent WJ, et al. Ontology application and use at the ENCODE DCC. Database : the Journal of Biological Databases and Curation. 2015. PMID 25776021 DOI: 10.1093/Database/Bav010  0.524
2015 Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Kent WJ, Haussler D, Paten B. Building a pan-genome reference for a population. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 22: 387-401. PMID 25565268 DOI: 10.1089/Cmb.2014.0146  0.591
2015 Rosenbloom KR, Armstrong J, Barber GP, Casper J, Clawson H, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hickey G, Hinrichs AS, Hubley R, ... ... Kent WJ, et al. The UCSC Genome Browser database: 2015 update. Nucleic Acids Research. 43: D670-81. PMID 25428374 DOI: 10.1093/Nar/Gku1177  0.645
2015 Haeussler M, Raney BJ, Hinrichs AS, Clawson H, Zweig AS, Karolchik D, Casper J, Speir ML, Haussler D, Kent WJ. Navigating protected genomics data with UCSC Genome Browser in a Box. Bioinformatics (Oxford, England). 31: 764-6. PMID 25348212 DOI: 10.1093/Bioinformatics/Btu712  0.579
2015 Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Kent WJ, Haussler D, Paten B. Building a pan-genome reference for a population Journal of Computational Biology. 22: 387-401. DOI: 10.1089/cmb.2014.0146  0.369
2014 Haeussler M, Karolchik D, Clawson H, Raney BJ, Rosenbloom KR, Fujita PA, Hinrichs AS, Speir ML, Eisenhart C, Zweig AS, Haussler D, Kent WJ. The UCSC Ebola Genome Portal. Plos Currents. 6. PMID 25685613 DOI: 10.1371/Currents.Outbreaks.386Ab0964Ab4D6C8Cb550Bfb6071D822  0.624
2014 Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, ... ... Kent WJ, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 515: 355-64. PMID 25409824 DOI: 10.1038/Nature13992  0.557
2014 Earl D, Nguyen N, Hickey G, Harris RS, Fitzgerald S, Beal K, Seledtsov I, Molodtsov V, Raney BJ, Clawson H, Kim J, Kemena C, Chang JM, Erb I, Poliakov A, ... ... Kent WJ, et al. Alignathon: a competitive assessment of whole-genome alignment methods. Genome Research. 24: 2077-89. PMID 25273068 DOI: 10.1101/Gr.174920.114  0.409
2014 Nguyen N, Hickey G, Raney BJ, Armstrong J, Clawson H, Zweig A, Karolchik D, Kent WJ, Haussler D, Paten B. Comparative assembly hubs: web-accessible browsers for comparative genomics. Bioinformatics (Oxford, England). 30: 3293-301. PMID 25138168 DOI: 10.1093/Bioinformatics/Btu534  0.524
2014 Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hinrichs AS, Learned K, Lee BT, ... ... Kent WJ, et al. The UCSC Genome Browser database: 2014 update. Nucleic Acids Research. 42: D764-70. PMID 24270787 DOI: 10.1093/Nar/Gkt1168  0.669
2014 Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, Karolchik D, Kent WJ. Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser Bioinformatics. 30: 1003-1005. PMID 24227676 DOI: 10.1093/Bioinformatics/Btt637  0.575
2014 Nguyen N, Hickey G, Raney BJ, Armstrong J, Clawson H, Zweig A, Karolchik D, Kent WJ, Haussler D, Paten B. Comparative assembly hubs: Web-accessible browsers for comparative genomics Bioinformatics. 30: 3293-3301. DOI: 10.1093/bioinformatics/btu534  0.468
2013 Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, Wong MC, Maddren M, Fang R, Heitner SG, Lee BT, Barber GP, Harte RA, Diekhans M, Long JC, ... ... Kent WJ, et al. ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Research. 41: D56-63. PMID 23193274 DOI: 10.1093/Nar/Gks1172  0.597
2013 Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Raney BJ, Pohl A, Malladi VS, Li CH, Lee BT, ... ... Kent WJ, et al. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Research. 41: D64-9. PMID 23155063 DOI: 10.1093/Nar/Gks1048  0.649
2013 Kuhn RM, Haussler D, Kent WJ. The UCSC genome browser and associated tools. Briefings in Bioinformatics. 14: 144-61. PMID 22908213 DOI: 10.1093/Bib/Bbs038  0.638
2012 Karolchik D, Hinrichs AS, Kent WJ. The UCSC Genome Browser. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit1.4. PMID 23255150 DOI: 10.1002/0471250953.Bi0104S00  0.665
2012 Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, ... ... Kent WJ, et al. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biology. 13: 418. PMID 22889292 DOI: 10.1186/Gb-2012-13-8-418  0.506
2012 Rosenbloom KR, Dreszer TR, Long JC, Malladi VS, Sloan CA, Raney BJ, Cline MS, Karolchik D, Barber GP, Clawson H, Diekhans M, Fujita PA, Goldman M, Gravell RC, Harte RA, ... ... Kent WJ, et al. ENCODE whole-genome data in the UCSC Genome Browser: update 2012. Nucleic Acids Research. 40: D912-7. PMID 22075998 DOI: 10.1093/Nar/Gkr1012  0.613
2011 Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, ... ... Kent WJ, et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 478: 476-82. PMID 21993624 DOI: 10.1038/Nature10530  0.484
2011 Karolchik D, Hinrichs AS, Kent WJ. The UCSC Genome Browser. Current Protocols in Human Genetics / Editorial Board, Jonathan L. Haines ... [Et Al.]. Unit18.6. PMID 21975940 DOI: 10.1002/0471142905.hg1806s71  0.594
2011 Sanborn JZ, Benz SC, Craft B, Szeto C, Kober KM, Meyer L, Vaske CJ, Goldman M, Smith KE, Kuhn RM, Karolchik D, Kent WJ, Stuart JM, Haussler D, Zhu J. The UCSC Cancer Genomics Browser: update 2011. Nucleic Acids Research. 39: D951-9. PMID 21059681 DOI: 10.1093/Nar/Gkq1113  0.562
2011 Raney BJ, Cline MS, Rosenbloom KR, Dreszer TR, Learned K, Barber GP, Meyer LR, Sloan CA, Malladi VS, Roskin KM, Suh BB, Hinrichs AS, Clawson H, Zweig AS, Kirkup V, ... ... Kent WJ, et al. ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic Acids Research. 39: D871-5. PMID 21037257 DOI: 10.1093/Nar/Gkq1017  0.586
2011 Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, ... ... Kent WJ, et al. The UCSC Genome Browser database: update 2011. Nucleic Acids Research. 39: D876-82. PMID 20959295 DOI: 10.1093/Nar/Gkq963  0.623
2010 Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, ... ... Kent WJ, et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (New York, N.Y.). 330: 1775-87. PMID 21177976 DOI: 10.1126/Science.1196914  0.515
2010 Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, ... ... Kent W, et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (New York, N.Y.). 330: 1787-97. PMID 21177974 DOI: 10.1126/Science.1198374  0.429
2010 Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics (Oxford, England). 26: 2204-7. PMID 20639541 DOI: 10.1093/bioinformatics/btq351  0.331
2010 Rosenbloom KR, Dreszer TR, Pheasant M, Barber GP, Meyer LR, Pohl A, Raney BJ, Wang T, Hinrichs AS, Zweig AS, Fujita PA, Learned K, Rhead B, Smith KE, Kuhn RM, ... ... Kent WJ, et al. ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Research. 38: D620-5. PMID 19920125 DOI: 10.1093/Nar/Gkp961  0.63
2010 Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, Pohl A, Pheasant M, Meyer LR, Learned K, Hsu F, ... ... Kent WJ, et al. The UCSC Genome Browser database: update 2010. Nucleic Acids Research. 38: D613-9. PMID 19906737 DOI: 10.1093/Nar/Gkp939  0.644
2010 Harte RA, Karolchik D, Kuhn RM, Kent WJ, Haussler D. Databases and genome browsers Vogel and Motulsky's Human Genetics: Problems and Approaches (Fourth Edition). 905-921. DOI: 10.1007/978-3-540-37654-5_44  0.587
2009 Karolchik D, Hinrichs AS, Kent WJ. The UCSC Genome Browser. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit1.4. PMID 19957273 DOI: 10.1002/0471250953.Bi0104S28  0.651
2009 Zhu J, Sanborn JZ, Benz S, Szeto C, Hsu F, Kuhn RM, Karolchik D, Archie J, Lenburg ME, Esserman LJ, Kent WJ, Haussler D, Wang T. The UCSC Cancer Genomics Browser. Nature Methods. 6: 239-40. PMID 19333237 DOI: 10.1038/Nmeth0409-239  0.478
2009 Cline MS, Kent WJ. Understanding genome browsing. Nature Biotechnology. 27: 153-5. PMID 19204697 DOI: 10.1038/Nbt0209-153  0.565
2009 Kuhn RM, Karolchik D, Zweig AS, Wang T, Smith KE, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pheasant M, Meyer L, Hsu F, Hinrichs AS, Harte RA, Giardine B, ... ... Kent WJ, et al. The UCSC Genome Browser Database: update 2009. Nucleic Acids Research. 37: D755-61. PMID 18996895 DOI: 10.1093/Nar/Gkn875  0.599
2008 Baertsch R, Diekhans M, Kent WJ, Haussler D, Brosius J. Retrocopy contributions to the evolution of the human genome. Bmc Genomics. 9: 466. PMID 18842134 DOI: 10.1186/1471-2164-9-466  0.521
2008 Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ. UCSC genome browser tutorial. Genomics. 92: 75-84. PMID 18514479 DOI: 10.1016/J.Ygeno.2008.02.003  0.621
2008 Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA, Hinrichs AS, Hsu F, Kober KM, Miller W, Pedersen JS, Pohl A, Raney BJ, ... ... Kent WJ, et al. The UCSC Genome Browser Database: 2008 update. Nucleic Acids Research. 36: D773-9. PMID 18086701 DOI: 10.1093/Nar/Gkm966  0.594
2007 Karolchik D, Hinrichs AS, Kent WJ. The UCSC Genome Browser. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 1.4. PMID 18428780 DOI: 10.1002/0471250953.bi0104s17  0.517
2007 Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, Hodges E, ... ... Kent WJ, et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 450: 219-32. PMID 17994088 DOI: 10.1038/Nature06340  0.535
2007 Karolchik D, Bejerano G, Hinrichs AS, Kuhn RM, Miller W, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ. Comparative genomic analysis using the UCSC genome browser. Methods in Molecular Biology (Clifton, N.J.). 395: 17-34. PMID 17993665 DOI: 10.1007/978-1-59745-514-5_2  0.575
2007 Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, Kosakovsky Pond SL, Nekrutenko A, Giardine B, Harris RS, Tyekucheva S, ... ... Kent WJ, et al. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Research. 17: 1797-808. PMID 17984227 DOI: 10.1101/Gr.6761107  0.628
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Kent WJ, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  0.6
2007 Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, ... ... Kent WJ, et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research. 17: 760-74. PMID 17567995 DOI: 10.1101/Gr.6034307  0.569
2007 Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, ... ... Kent WJ, et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science (New York, N.Y.). 316: 222-34. PMID 17431167 DOI: 10.1126/Science.1139247  0.574
2007 Thomas DJ, Rosenbloom KR, Clawson H, Hinrichs AS, Trumbower H, Raney BJ, Karolchik D, Barber GP, Harte RA, Hillman-Jackson J, Kuhn RM, Rhead BL, Smith KE, Thakkapallayil A, Zweig AS, ... ... Kent WJ, et al. The ENCODE Project at UC Santa Cruz. Nucleic Acids Research. 35: D663-7. PMID 17166863 DOI: 10.1093/Nar/Gkl1017  0.547
2007 Thomas DJ, Trumbower H, Kern AD, Rhead BL, Kuhn RM, Haussler D, Kent WJ. Variation resources at UC Santa Cruz. Nucleic Acids Research. 35: D716-20. PMID 17151077 DOI: 10.1093/Nar/Gkl953  0.585
2007 Kuhn RM, Karolchik D, Zweig AS, Trumbower H, Thomas DJ, Thakkapallayil A, Sugnet CW, Stanke M, Smith KE, Siepel A, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pedersen JS, ... ... Kent WJ, et al. The UCSC genome browser database: update 2007. Nucleic Acids Research. 35: D668-73. PMID 17142222 DOI: 10.1093/Nar/Gkl928  0.589
2006 Ma J, Zhang L, Suh BB, Raney BJ, Burhans RC, Kent WJ, Blanchette M, Haussler D, Miller W. Reconstructing contiguous regions of an ancestral genome. Genome Research. 16: 1557-65. PMID 16983148 DOI: 10.1101/Gr.5383506  0.54
2006 Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature. 441: 87-90. PMID 16625209 DOI: 10.1038/Nature04696  0.558
2006 Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, Haussler D. The UCSC Known Genes. Bioinformatics (Oxford, England). 22: 1036-46. PMID 16500937 DOI: 10.1093/Bioinformatics/Btl048  0.561
2006 Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM, Pedersen JS, Pohl A, Raney BJ, ... ... Kent WJ, et al. The UCSC Genome Browser Database: update 2006. Nucleic Acids Research. 34: D590-8. PMID 16381938 DOI: 10.1093/Nar/Gkj144  0.606
2006 DiBiase A, Harte RA, Zhou Y, Zon L, Kent WJ. Piloting the zebrafish genome browser. Developmental Dynamics : An Official Publication of the American Association of Anatomists. 235: 747-53. PMID 16372332 DOI: 10.1002/Dvdy.20661  0.613
2005 Bejerano G, Siepel AC, Kent WJ, Haussler D. Computational screening of conserved genomic DNA in search of functional noncoding elements. Nature Methods. 2: 535-45. PMID 16170870 DOI: 10.1038/Nmeth0705-535  0.574
2005 Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A. Galaxy: a platform for interactive large-scale genome analysis. Genome Research. 15: 1451-5. PMID 16169926 DOI: 10.1101/Gr.4086505  0.491
2005 Mikkelsen TS, Hillier LW, Eichler EE, Zody MC, Jaffe DB, Yang S, Enard W, Hellmann I, Lindblad-Toh K, Altheide TK, Archidiacono N, Bork P, Butler J, Chang JL, Cheng Z, ... ... Kent WJ, et al. Initial sequence of the chimpanzee genome and comparison with the human genome Nature. 437: 69-87. PMID 16136131 DOI: 10.1038/Nature04072  0.626
2005 Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Research. 15: 1034-50. PMID 16024819 DOI: 10.1101/Gr.3715005  0.551
2005 Kent WJ, Hsu F, Karolchik D, Kuhn RM, Clawson H, Trumbower H, Haussler D. Exploring relationships and mining data with the UCSC Gene Sorter. Genome Research. 15: 737-41. PMID 15867434 DOI: 10.1101/Gr.3694705  0.489
2005 Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, et al. Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology. 23: 137-44. PMID 15637633 DOI: 10.1038/Nbt1053  0.305
2005 Hsu F, Pringle TH, Kuhn RM, Karolchik D, Diekhans M, Haussler D, Kent WJ. The UCSC Proteome Browser. Nucleic Acids Research. 33: D454-8. PMID 15608236 DOI: 10.1093/Nar/Gki100  0.583
2004 Ao W, Gaudet J, Kent WJ, Muttumu S, Mango SE. Environmentally induced foregut remodeling by PHA-4/FoxA and DAF-12/NHR. Science (New York, N.Y.). 305: 1743-6. PMID 15375261 DOI: 10.1126/Science.1102216  0.431
2004 Chen J, Sun M, Kent WJ, Huang X, Xie H, Wang W, Zhou G, Shi RZ, Rowley JD. Over 20% of human transcripts might form sense-antisense pairs. Nucleic Acids Research. 32: 4812-20. PMID 15356298 DOI: 10.1093/Nar/Gkh818  0.505
2004 Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D. Ultraconserved elements in the human genome. Science (New York, N.Y.). 304: 1321-5. PMID 15131266 DOI: 10.1126/Science.1098119  0.609
2004 Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Research. 14: 708-15. PMID 15060014 DOI: 10.1101/Gr.1933104  0.586
2004 Bailey JA, Baertsch R, Kent WJ, Haussler D, Eichler EE. Hotspots of mammalian chromosomal evolution. Genome Biology. 5: R23. PMID 15059256 DOI: 10.1186/Gb-2004-5-4-R23  0.536
2004 Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, ... ... Kent WJ, et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 428: 493-521. PMID 15057822 DOI: 10.1038/Nature02426  0.53
2004 Sugnet CW, Kent WJ, Ares M, Haussler D. Transcriptome and genome conservation of alternative splicing events in humans and mice. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 66-77. PMID 14992493  0.39
2004 Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. The UCSC Table Browser data retrieval tool. Nucleic Acids Research. 32: D493-6. PMID 14681465 DOI: 10.1093/Nar/Gkh103  0.581
2003 Chiaromonte F, Weber RJ, Roskin KM, Diekhans M, Kent WJ, Haussler D. The share of human genomic DNA under selection estimated from human-mouse genomic alignments. Cold Spring Harbor Symposia On Quantitative Biology. 68: 245-54. PMID 15338624  0.439
2003 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proceedings of the National Academy of Sciences of the United States of America. 100: 11484-9. PMID 14500911 DOI: 10.1073/Pnas.1932072100  0.607
2003 Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, Margulies EH, Blanchette M, Siepel AC, Thomas PJ, McDowell JC, Maskeri B, Hansen NF, Schwartz MS, Weber RJ, Kent WJ, et al. Comparative analyses of multi-species sequences from targeted genomic regions. Nature. 424: 788-93. PMID 12917688 DOI: 10.1038/Nature01858  0.566
2003 Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R, Wylie K, Sekhon M, Becker MC, O'Laughlin MD, Schaller ME, ... ... Kent WJ, et al. The DNA sequence of human chromosome 7. Nature. 424: 157-64. PMID 12853948 DOI: 10.1038/Nature01782  0.465
2003 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Research. 13: 103-7. PMID 12529312 DOI: 10.1101/Gr.809403  0.607
2003 Hardison RC, Roskin KM, Yang S, Diekhans M, Kent WJ, Weber R, Elnitski L, Li J, O'Connor M, Kolbe D, Schwartz S, Furey TS, Whelan S, Goldman N, Smit A, et al. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Research. 13: 13-26. PMID 12529302 DOI: 10.1101/Gr.844103  0.463
2003 Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, Weber RJ, Haussler D, Kent WJ. The UCSC Genome Browser Database. Nucleic Acids Research. 31: 51-4. PMID 12519945 DOI: 10.1093/Nar/Gkg129  0.584
2002 Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, ... ... Kent WJ, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420: 520-62. PMID 12466850 DOI: 10.1038/Nature01262  0.654
2002 Farrer T, Roller AB, Kent WJ, Zahler AM. Analysis of the role of Caenorhabditis elegans GC-AG introns in regulated splicing. Nucleic Acids Research. 30: 3360-7. PMID 12140320 DOI: 10.1093/Nar/Gkf465  0.659
2002 Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Research. 12: 996-1006. PMID 12045153 DOI: 10.1101/Gr.229102  0.766
2002 Kent WJ. BLAT--the BLAST-like alignment tool. Genome Research. 12: 656-64. PMID 11932250 DOI: 10.1101/Gr.229202  0.621
2001 Kent WJ, Haussler D. Assembly of the working draft of the human genome with GigAssembler. Genome Research. 11: 1541-8. PMID 11544197 DOI: 10.1101/Gr.183201  0.614
2001 McPherson JD, Marra M, Hillier L, Waterston RH, Chinwalla A, Wallis J, Sekhon M, Wylie K, Mardis ER, Wilson RK, Fulton R, Kucaba TA, Wagner-McPherson C, Barbazuk WB, Gregory SG, ... ... Kent WJ, et al. A physical map of the human genome. Nature. 409: 934-41. PMID 11237014 DOI: 10.1038/35057157  0.578
2001 Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, ... ... Kent WJ, et al. Initial sequencing and analysis of the human genome. Nature. 409: 860-921. PMID 11237011 DOI: 10.1038/35057062  0.613
2001 Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, Fitzhugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, ... ... Kent WJ, et al. Erratum: Initial sequencing and analysis of the human genome: International Human Genome Sequencing Consortium (Nature (2001) 409 (860-921)) Nature. 412: 565-566. DOI: 10.1038/35087627  0.61
2000 Kent WJ, Zahler AM. Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. Genome Research. 10: 1115-25. PMID 10958630 DOI: 10.1101/Gr.10.8.1115  0.724
2000 Kent WJ, Zahler AM. The intronerator: exploring introns and alternative splicing in Caenorhabditis elegans. Nucleic Acids Research. 28: 91-3. PMID 10592190 DOI: 10.1093/Nar/28.1.91  0.705
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